QM/MM Study of the Mechanism of the Noncanonical S-Cγ Bond Scission in S-Adenosylmethionine Catalyzed by the CmnDph2 Radical Enzyme

In nature, the radical SAM enzyme family plays a fascinating role in the radical chemistry, and the majority of them catalyze the cleavage of the S-C5′ bond to initiate the radical-based catalysis. Diphthamide biosynthesis protein 2 is a notable member of this superfamily, which cleaves the inert S-Cγ bond of SAM, leading to a new organometallic [4Fe-4S]-alkyl complex, expanding the mechanisms of radical SAM enzymes. In this work, we performed QM/MM calculations to elucidate the mechanism for the formation of the organometallic [4Fe-4S]-alkyl complex by the S-Cγ bond cleavage. All six possible antiferromagnetically-coupled spin states (ααββ, αβαβ, αββα, ββαα, βαβα, βααβ) were considered, the calculations showed that the reactant is at the αβαβ state, while the transition state is at the βααβ state, the product is the ααββ state. The most favorable pathway was found to be concerted, namely S-Cγ bond cleavage coupled with the Fe-Cγ bond formation, which is associated with a barrier of 25.7 kcal/mol. During the reaction, one electron is transferred from the two beta spin ferrous ions to the S-Cγ σ* orbital, which triggers the S-C bond cleavage. Importantly, the substrate coordinated iron ion prefers to be a ferrous ion and have a beta spin to facilitate the substrate activation. The present results should be helpful for the understanding of related [4Fe-4S] cluster dependent enzymatic reactions.